Vlaar made his professional debut at the age of 20 for the club AZ. After a successful 2005 FIFA World Youth Championship with Netherlands U20, Vlaar received his first call-up for the Netherlands national team by the Netherlands coach Marco van Basten. Despite the few but promising matches Vlaar played, the youngster was transferred to Feyenoord. Main reason for his move was his personal relationship with AZ coach Louis van Gaal. Vlaar was often compared to Jaap Stam, but due to various injuries the centre back couldn't live up to the expectations as of yet.

Vlaar was an important player in the two Netherlands U21 squads winning the UEFA European Under-21 Football Championship in 2006 and 2007.